Phylogenetic Diversity of <i>Trichoderma</i> Strains and Their Antagonistic Potential against Soil-Borne Pathogens under Stress Conditions

<i>Trichoderma</i> species are known as excellent biocontrol agents against soil-borne pathogens that cause considerable crop losses. Eight strains of <i>Trichoderma</i> were isolated from five Egyptian regions. They identified based on translation elongation factor-1α (<i>TEF1</i>) sequencing as four different <i>Trichoderma</i> species: <i>Trichoderma asperellum</i>, <i>Trichoderma harzianum</i>, <i>Trichoderma viride</i>, and <i>Trichoderma longibrachiatum</i>. Optimal growth conditions (temperature and media), and the phosphate solubilization capability of <i>Trichoderma</i> strains were evaluated in vitro. Further, the ability of these strains to antagonize <i>Fusarium solani</i>, <i>Macrophomina phaseolina</i>, and <i>Fusarium graminearum</i> was also evaluated. The results revealed that <i>Trichoderma harzianum</i> (<i>Th6</i>) exhibited the highest antagonistic ability against <i>F. solani</i>, <i>M. phaseolina</i> and <i>F. graminearum</i> with inhibition rates of 71.42%, 72.97%, and 84.61%, respectively. <i>Trichoderma viride</i> (<i>Tv8</i>) exhibited the lowest antagonism against the same pathogens with inhibition rates of 50%, 64% and 69.23%, respectively. Simple-sequence repeats (SSRs) and random amplified polymorphic DNA (RAPD) markers were used to evaluate the genetic variability of the <i>Trichoderma</i> strains. The results revealed that of 45 RAPD amplified bands, 36 bands (80%) were polymorphic and of SSRs amplified 36 bands, 31 bands (86.11%) were polymorphic. The amplification of calmodulin and <i>β-1,3-endoglucanase</i> was noted at 500 bp and 230 bp, respectively. Data indicated that <i>T. viride</i> (<i>Tv8</i>) had the highest phosphate solubilization index (10.0 mm), while <i>T. harzianum</i> (<i>Th6</i>) had the lowest phosphate solubilization index (4.0 mm). In conclusion, <i>T. harzianum</i> (<i>Th6</i>) had the highest antagonistic activity in dual culture assay along with the growth rate; while <i>T. viride</i> (<i>Tv8</i>) had the highest phosphate solubilization activity. There are still gaps in obtaining new formulations, selecting potent <i>Trichoderma</i> strains to confirm disease control in planta. For improving <i>Trichoderma</i> recommendation in the organic agricultural system and sustaining the fertility of the soil, the field application of highly antagonistic biocontrol agents in different types of soil and plant species will be the first approach toward bio-pesticide treatments along with bio-fertilizer inoculation. Furthermore, secondary metabolites will be investigated for the most promising strains with the combination of different pathogens and application timing.